The long-term objective of this application is to uncover the characteristics of a group of bacteria called the lactobacilli (Lb) that play a key role in the progression and severity of dental caries in both children and adults. For almost a century, the link between caries and Lb was known, but further progress in delineating which of the more than 100 species of lactobacilli were responsible for dental caries remained elusive. Recent advances in genetic methods and the publication of a dozen Lb genomes now make it possible to gain important insight into the sub-group of Lb members and the cariogenic traits responsible for caries. These goals will be met by two specific aims. Aim 1 is to conduct a survey of the Lb populations in three groups of children, those with severe early childhood caries (S-ECC) and two comparison groups, a caries free (CF) and a moderately active caries (white spot lesion, WSL) group. We will accomplish these aims by both culture-independent and culture-dependent methods to obtain estimates of abundance and diversity of the Lb populations. We will also identify individual Lb genotypes found in the three groups by AP-PCR. Lb species identification of unique genotypes will be accomplished by 16S rRNA gene sequencing to obtain a collection of isolates that represent the different species/genotypes that characterize the S-ECC, WSL, and CF habitat or niche. Aim 2 is to identify genetic attributes associated with the caries-niche. A combination of whole-genome sequencing and comparative genomics applied to the isolates derived from Aim 1, coupled with non-oral Lb genome sequences available in public and private database, will result in the identification of genetic signatures unique to the caries/caries-free niche. With this information, clinicians will be able to analyze a bacterial sample from the mouth and determine whether the Lb present are cariogenic or not. This, in turn, will give clinicians an estimation of risk for, and severity of, dental caries. An important spin off to these findings will pave the way toward assessing the cariogenic potential of Lb proposed as health-associated probiotics. PUBLIC HEALTH RELEVANCE: Lactobacilli (Lb) share many characteristics of cariogenic bacteria with the mutans streptococci (MS), including a high prevalence in caries lesions and the ability to generate a low pH environment as well as to survive in it. However, little is known about the natural history, diversity, distribution, and sources of specific species of Lb associated with dental caries. Out of the hundreds of Lb species described thus far, only a handful have been consistently found in the oral cavity and, in particular, associated with dental caries. This raises the question about common attributes that may allow these species to thrive in the oral cavity and, more specifically, determine the progress and severity of dental caries. The proposed study will answer those questions using a combination of well- established microbiologic and genotyping techniques, with next-generation sequencing and whole- genome comparison. Future caries risk assessments, therefore, may include not only Lb counts, but also a measure reflecting their cariogenic potential based on the presence/absence of certain species and/or certain caries-specific genetic elements. This can also be used to indicate how well caries lesions have been restored and retentive areas eliminated. Rendering the mouth Lb-free may become a major objective of dental treatment.